Epidemiologic Profile of Severe Acute Respiratory Infection in Brazil During the COVID-19 Pandemic: An Epidemiological Study

The determinants of COVID-19 case reporting across Africa

Background

According to study on the under-estimation of COVID-19 cases in African countries, the average daily case reporting rate was only 5.37% in the initial phase of the outbreak when there was little or no control measures. In this work, we aimed to identify the determinants of the case reporting and classify the African countries using the case reporting rates and the significant determinants.

Methods

We used the COVID-19 daily case reporting rate estimated in the previous paper for 54 African countries as the response variable and 34 variables from demographics, socioeconomic, religion, education, and public health categories as the predictors. We adopted a generalized additive model with cubic spline for continuous predictors and linear relationship for categorical predictors to identify the significant covariates. In addition, we performed Hierarchical Clustering on Principal Components (HCPC) analysis on the reporting rates and significant continuous covariates of all countries.

Results

21 covariates were identified as significantly associated with COVID-19 case detection: total population, urban population, median age, life expectancy, GDP, democracy index, corruption, voice accountability, social media, internet filtering, air transport, human development index, literacy, Islam population, number of physicians, number of nurses, global health security, malaria incidence, diabetes incidence, lower respiratory and cardiovascular diseases prevalence. HCPC resulted in three major clusters for the 54 African countries: northern, southern and central essentially, with the northern having the best early case detection, followed by the southern and the central.

Conclusion

Overall, northern and southern Africa had better early COVID-19 case identification compared to the central. There are a number of demographics, socioeconomic, public health factors that exhibited significant association with the early case detection.

Overview of the Indigenous health of the Yanomami ethnic group in Brazil: A Public Health Emergency

INTRODUCTION

The Indigenous population of the Yanomami ethnic group in Brazil is currently facing a public health emergency due to the high number of deaths, mainly of children. Taking that into consideration, this study aims to analyze this crisis impact on the health of this population in the period between 2018 and 2022.

METHODS

The data presented were collected from the report called Yanomami Mission ("Missão Yanomami") published by the Brazilian Ministry of Health and, from it, a descriptive analysis of the Indigenous individuals' health was carried out for (i) the geographical distribution; ii) the number of deaths; (iii) the child death rate; (iv) the deaths of Indigenous individuals from preventable causes; (v) the causes of preventable diseases related to hygiene and basic sanitation, and the distribution of diarrheal diseases according to age groups; (vi) evaluation of the nutritional classification; vii) the percentage (%) of the complete vaccination scheme, and (viii) the coverage of prenatal appointments of Indigenous pregnant women.

RESULTS

The report included 31,017 individuals belonging to the Yanomami ethnic group, most of the participants were up to 39 years old (N = 26,377; 85.0%) and men (N = 15,836; 51.1%). During the period described in the report, the number of deaths reached 1285/31,017 (4.1%). When analyzing the deaths, the most representative age groups were those of children under 1 year old (505/1285; 39.9%), from 1 to 4 years old (178/1285; 13.8%), and the elderly from 60 to 79 years old (150/1285; 11.6%). The Indigenous individuals from this ethnic group presented a child death rate ~ 1.5 to 3.5 higher than that of the total Indigenous population in the country. Regarding the child death rate, the neonatal component represented 57.8% of the deaths and, in 2022, 93.0% of the pregnant women had less than six prenatal appointments. This population shows a high number of deaths due to preventable causes (N = 538) and cases of illnesses associated with hygiene and sanitation, for example (N = 35,103 cases/notifications). As for vaccination, the full vaccination scheme targeting children below 5 years old has not been met since 2018.

CONCLUSION

In the Indigenous population of the Yanomami ethnic group, a high number of deaths was observed, which affected mainly individuals under 1 year old. Among the factors associated with the deaths, mainly in children under 5 years old, most cases have preventable causes, which could be reduced by proper action promoting their health and preventing diseases.

Factors associated with COVID-19 among hospitalized patients with severe acute respiratory infections in Serbia, 2022-2023: A test negative case-control study

Severe acute respiratory infections (SARI) are estimated to be the cause of death in about 19% of all children younger than 5 years globally. The outbreak of coronaviral disease (COVID-19) caused by SARS-CoV-2, increased considerably the burden of SARI worldwide. We used data from a vaccine effectiveness study to identify the factors associated with SARS CoV-2 infection among hospitalized SARI patients. We recruited SARI patients at 3 hospitals in Serbia from 7 April 2022-1 May 2023. We collected demographic and clinical data from patients using a structured questionnaire, and all SARI patients were tested for SARS-CoV-2 by RT-PCR. We conducted an unmatched test negative case-control study. SARS-CoV-2 infected SARI patients were considered cases, while SARS CoV-2 negative SARI patients were controls. We conducted bivariate and multivariable logistic regression analysis in order to identify variables associated with SARS-CoV-2 infection. We included 110 SARI patients: 74 were cases and 36 controls. We identified 5 factors associated with SARS-CoV-2 positivity, age (OR  =  1.04; 95% CI  =  1.01-1.07), having received primary COVID-19 vaccine series (OR  =  0.28; 95% CI  =  0.09-0.88), current smoking (OR  =  8.64; 95% CI  =  2.43-30.72), previous SARS CoV-2 infection (OR  =  3.48; 95% CI  =  1.50-8.11) and number of days before seeking medical help (OR  =  0.81; 95% CI  =  0.64-1.02). In Serbia during a period of Omicron circulation, we found that older age, unvaccinated, hospitalized SARI patients, previously infected with SARS CoV-2 virus and those who smoked, were more likely to be SARS-CoV-2-positive; these patient populations should be prioritized for COVID vaccination.

Dichotomous outcomes vs. survival regression models for identification of predictors of mortality among patients with severe acute respiratory illness during COVID-19 pandemics

Introduction

As the studies predicting mortality in severe acute respiratory illness (SARI) have inferred associations either from dichotomous outcomes or from time-event models, we identified some clinical-epidemiological characteristics and predictors of mortality by comparing and discussing two multivariate models.

Methods

To identify factors associated with death among all SARI hospitalizations occurred in Botucatu (Brazil)/regardless of the infectious agent, and among the COVID-19 subgroup, from March 2020 to 2022, we used a multivariate Poisson regression model with binomial outcomes and Cox proportional hazards (time-event). The performance metrics of both models were also analyzed.

Results

A total of 3,995 hospitalized subjects were included, of whom 1338 (33%) tested positive for SARS-CoV-2. We identified 866 deaths, of which 371 (43%) were due to the COVID-19. In the total number of SARI cases, using both Poisson and Cox models, the predictors of mortality were the presence of neurological diseases, immunosuppression, obesity, older age, and need for invasive ventilation support. However, the Poisson test also revealed that admission to an intensive care unit and the COVID-19 diagnosis were predictors of mortality, with the female gender having a protective effect against death. Likewise, Poisson proved to be more sensitive and specific, and indeed the most suitable model for analyzing risk factors for death in patients with SARI/COVID-19.

Conclusion

Given these results and the acute course of SARI and COVID-19, to compare the associations and their different meanings is essential and, therefore, models with dichotomous outcomes are more appropriate than time-to-event/survival approaches.

COVID-19 in Brazil: a 3-year update

Three years into the coronavirus disease (COVID)-19 pandemic and the world is still struggling with the aftermath of this global health crisis. In Brazil, we are witnessing serious economic, health, social, and political problems. The rapid spread of the virus in our country was the result of a shortage of vaccines and the lack of an effective national campaign to identify and report cases. This health crisis also intensified social inequalities, hitting Indigenous peoples hard due to the lack of access to health services. In addition, rising unemployment and overcrowding of the health system made contagion possible, especially among the most vulnerable, increasing the number of serious cases of the disease. It is important to highlight that emotional problems worsened, the educational system was severely affected, and domestic violence increased during the confinement period, in addition to the fact that the pandemic exposed the great disparities of regional inequalities that exist across the country, mainly concerning health management.

SIRSi-vaccine dynamical model for the Covid-19 pandemic

Covid-19, caused by severe acute respiratory syndrome coronavirus 2, broke out as a pandemic during the beginning of 2020. The rapid spread of the disease prompted an unprecedented global response involving academic institutions, regulatory agencies, and industries. Vaccination and nonpharmaceutical interventions including social distancing have proven to be the most effective strategies to combat the pandemic. In this context, it is crucial to understand the dynamic behavior of the Covid-19 spread together with possible vaccination strategies. In this study, a susceptible-infected-removed-sick model with vaccination (SIRSi-vaccine) was proposed, accounting for the unreported yet infectious. The model considered the possibility of temporary immunity following infection or vaccination. Both situations contribute toward the spread of diseases. The transcritical bifurcation diagram of alternating and mutually exclusive stabilities for both disease-free and endemic equilibria were determined in the parameter space of vaccination rate and isolation index. The existing equilibrium conditions for both points were determined in terms of the epidemiological parameters of the model. The bifurcation diagram allowed us to estimate the maximum number of confirmed cases expected for each set of parameters. The model was fitted with data from São Paulo, the state capital of SP, Brazil, which describes the number of confirmed infected cases and the isolation index for the considered data window. Furthermore, simulation results demonstrate the possibility of periodic undamped oscillatory behavior of the susceptible population and the number of confirmed cases forced by the periodic small-amplitude oscillations in the isolation index. The main contributions of the proposed model are as follows: A minimum effort was required when vaccination was combined with social isolation, while additionally ensuring the existence of equilibrium points. The model could provide valuable information for policymakers, helping define disease prevention mitigation strategies that combine vaccination and non-pharmaceutical interventions, such as social distancing and the use of masks. In addition, the SIRSi-vaccine model facilitated the qualitative assessment of information regarding the unreported infected yet infectious cases, while considering temporary immunity, vaccination, and social isolation index.

Respiratory Syncytial Virus: A Systematic Review and Meta-Analysis of Tomographic Findings (2000-2022)

Human respiratory syncytial virus (RSV) is a main cause of medical referrals and hospitalizations in all infants, particularly among newborns. Nevertheless, relatively limited evidence on chest tomography (CT) findings has been collected. According to the PRISMA statement, Pubmed, Embase, and medRxiv were searched for eligible observational studies published up to 31 December 2022. Cases were categorized in children and adolescents (age < 18 years), adults and elderly (age ≥ 18 years), and immunocompromised patients, and then pooled in a random-effects model. Heterogeneity was assessed using the I2 statistics, while reporting bias was assessed by means of funnel plots and regression analysis. A total of 10 studies (217 RSV cases) were retrieved (children, 37.3%; immunocompromised, 41.0%; adults, 21.7%). The most common features were signs of organizing pneumonia (33.65%, 95% confidence interval [95% CI] 22.39-47.27), followed by septal thickening (33.19%, 95% CI 21.76-47.03), ground glass opacities (GGOs; 28.03%, 95% CI 14.69-46.82), and tree-in-bud (TIB, 27.44%, 95% CI 15.04-44.68). Interestingly, up to 16.23% (95% CI 8.17-29.69) showed normal findings, while the large majority (76.06%, 95% CI 64.81-84.56) were characterized by bilateral involvement. Studies were highly heterogeneous without substantial reporting bias. Assuming children and adolescents as reference groups, healthy adults were characterized by a higher risk ratio [RR] for septal thickening (RR 3.878, 95% CI 1.253-12.000), nodular lesions (RR 20.197, 95% CI 1.286-317.082), and GGOs (RR 2.121, 95% CI 1.121-4.013). RSV cases are rarely assessed in terms of CT characteristics. Our study identified some specificities, suggesting that RSV infections evolve heterogeneous CT features in children/adolescents and adults, but the paucity of studies recommends a cautious appraisal.

Epidemiological Profile of Hospitalized Patients with Cystic Fibrosis in Brazil Due to Severe Acute Respiratory Infection during the COVID-19 Pandemic and a Systematic Review of Worldwide COVID-19 in Those with Cystic Fibrosis

Since the onset of the coronavirus disease, COVID-19 pandemic, concern arose for those who might be at higher risk of a worse COVID-19 prognosis, such as those with cystic fibrosis (CF). In this context, we evaluated the features of hospitalized patients with CF due to severe acute respiratory infection (SARI) in Brazil and we also performed a systematic review including all the studies published from the beginning of the first case of COVID-19 (17 November 2019) to the date of this search (23 May 2022) which included, concomitantly, patients with CF and COVID-19 in the worldwide population. In our Brazilian data, we evaluated the period from December 2019 to March 2022, and we included 33 demographical and clinical patients' features. We classified the patients into groups: (G1) SARI due to another viral infection than severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (23; 5.4%), (G2) SARI due to an unknown etiological agent (286; 67.1%), and (G3) SARI due to SARS-CoV-2 infection (117; 27.5%). The individuals in G3 tended to be older, especially over 50 years old, and presented a higher prevalence of dyspnea, peripheral capillary oxygen saturation (SpO₂) <95%, and cardiopathy. The highest prevalence for intensive care unit (ICU) treatment (52; 44.4%) and invasive mechanical ventilation (29; 24.8%) was for patients in G3. Almost half of the patients in G3 died (51; 43.6%); in contrast, none in G1 died. However, we observed 43 (15.0%) deaths in G2. In addition, 12 (4.2%) and one (0.9%) death not associated with SARI occurred, respectively, in the G2 and G3. The patients who died due to SARS-CoV-2 infection had a higher frequency of SpO₂ <95% (46; 90.2%), ICU treatment (34; 66.7%), and invasive mechanical ventilation (27; 52.9%) when compared to those who recovered. The systematic review comprised a total of 31 papers published as observational studies. These studies comprised 661,386 patients in total, including children, adults, and elderly age groups. However, only 19,150 (2.9%) patients were diagnosed with CF and, from these patients, 2523 (0.4%) were diagnosed with both CF and COVID-19. It was observed that the most common outcome was the need for hospitalization (n = 322 patients with CF), and the need for oxygen support (n = 139 patients with CF). One hundred patients with CF needed intensive care units, fifty patients needed non-invasive mechanical ventilation support, and only three patients were described as receiving invasive mechanical ventilation support. Deaths were described in 38 patients with CF. Importantly, lung-transplanted patients with CF represented an increased risk of death in one publication; in accordance, another study described that lung transplantation and moderate to severe lung disease were independent risk factors for severe outcomes after SARS-CoV-2 infection. In contrast with the literature, in conclusion, Brazilian patients in G3 presented a severe phenotype, even though most of the other studies did not observe worse outcomes in patients with CF and COVID-19.

Investigating the impact of CO2 emissions on the COVID-19 pandemic by generalized linear mixed model approach with inverse Gaussian and gamma distributions

Carbon dioxide (CO2) rate within the atmosphere has been rising for decades due to human activities especially due to usage of fuel types such as coal, cement, flaring, gas, oil, etc. Especially in 2020, COVID-19 pandemic caused major economic, production, and energy crises all around the world. As a result of this situation, there was a sharp decrease in the global CO2 emissions depending on the fuel types used during this pandemic. The aim of this study was to explore the effects of “CO2 emissions due to the fuel types” on “percentage of deaths in total cases” attributed to the COVID-19 pandemic using generalized linear model and generalized linear mixed model (GLMM) approaches with inverse Gaussian and gamma distributions, and also to obtain global statistical inferences about 169 World Health Organization member countries that will disclose the impact of the CO2 emissions due to the fuel types during this pandemic. The response variable is taken as “percentage of deaths in total cases attributed to the COVID-19 pandemic” calculated as “(total deaths/total confirmed cases attributed to the COVID-19 pandemic until December 31, 2020)*100.” The explanatory variables are taken as “production-based emissions of CO2 from different fuel types,” measured in tonnes per person, which are “coal, cement, flaring, gas, and oil.” As a result of this study, according to the goodness-of-fit test statistics, “GLMM approach with gamma distribution” called “gamma mixed regression model” is determined as the most appropriate statistical model for investigating the impact of CO2 emissions on the COVID-19 pandemic. As the main findings of this study, 1 t CO2 emissions belonging to the fuel types “cement, coal, flaring, gas, and oil” per person cause increase in deaths in total cases attributed to the COVID-19 pandemic by 2.8919, 2.6151, 2.5116, 2.5774, and 2.5640%, respectively.

Profile of coronavirus disease enlightened asthma as a protective factor against death: An epidemiology study from Brazil during the pandemic

INTRODUCTION

The possibility that asthma is not a risk factor for the worst outcomes due to coronavirus disease (COVID-19) is encouraged. The increase in Th2 response dominance can downregulate the late phase of hyperinflammation, which is typically the hallmark of more severe respiratory viral infections, alongside lower angiotensin-converting enzyme receptors in patients with asthma due to chronic inflammation. Few studies associated asthma diagnosis and COVID-19 outcomes. In this context, we aimed to associate the asthma phenotype with the clinical signs, disease progression, and outcomes in patients with COVID-19.

METHODS

We performed an epidemiologic study using patients' characteristics from OpenDataSUS to verify the severity of COVID-19 among Brazilian hospitalized patients with and without the asthma phenotype according to the need for intensive care units, intubation, and deaths. We also evaluated the demographic data (sex, age, place of residence, educational level, and race), the profile of clinical signs, and the comorbidities.

RESULTS

Asthma was present in 43,245/1,129,838 (3.8%) patients. Among the patients with asthma, 74.7% who required invasive ventilatory support evolved to death. In contrast, 78.0% of non-asthmatic patients who required invasive ventilatory support died (OR = 0.83; 95% CI = 0.79-0.88). Also, 20.0% of the patients with asthma that required non-invasive ventilatory support evolved to death, while 23.5% of non-asthmatic patients evolved to death (OR = 0.81; 95% CI = 0.79-0.84). Finally, only 11.2% of the patients with asthma who did not require any ventilatory support evolved to death, while 15.8% of non-asthmatic patients evolved to death (OR = 0.67; 95% CI = 0.62-0.72). In our multivariate analysis, one comorbidity and one clinical characteristic stood out as protective factors against death during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Patients with asthma were less prone to die than other patients (OR = 0.79; 95% CI = 0.73-0.85), just like puerperal patients (OR = 0.74; 95% CI = 0.56-0.97) compared to other patients.

CONCLUSION

Asthma was a protective factor for death in hospitalized patients with COVID-19 in Brazil. Despite the study's limitations on patients' asthma phenotype information and corticosteroid usage, this study brings to light information regarding a prevalent condition that was considered a risk factor for death in COVID-19, being ultimately protective.

Potential Use of Exhaled Breath Condensate for Diagnosis of SARS-CoV-2 Infections: A Systematic Review and Meta-Analysis

Background. Reverse-transcriptase polymerase chain reaction (RT-qPCR) assays performed on respiratory samples collected through nasal swabs still represent the gold standard for COVID-19 diagnosis. Alternative methods to this invasive and time-consuming options are still being inquired, including the collection of airways lining fluids through exhaled breath condensate (EBC). Materials and Methods. We performed a systematic review and meta-analysis in order to explore the reliability of EBC as a way to collect respiratory specimens for RT-qPCR for diagnosis of COVID-19. Results. A total of 4 studies (205 specimens), were ultimately collected, with a pooled sensitivity of 69.5% (95%CI 26.8–93.4), and a pooled specificity of 98.3% (95%CI 87.8–99.8), associated with high heterogeneity and scarce diagnostic agreement with the gold standard represented by nasal swabs (Cohen’s kappa = 0.585). Discussion. Even though non-invasive options for diagnosis of COVID-19 are still necessary, EBC-based RT-qPCR showed scarce diagnostic performances, ultimately impairing its implementation in real-world settings. However, as few studies have been carried out to date, and the studies included in the present review are characterized by low numbers and low sample power, further research are requested to fully characterize the actual reliability of EBC-based RT-qPCR in the diagnosis of COVID-19.